{"id":21274878,"url":"https://github.com/maayanlab/enrichmentapi","last_synced_at":"2025-08-15T00:36:25.937Z","repository":{"id":46132125,"uuid":"146011706","full_name":"MaayanLab/enrichmentAPI","owner":"MaayanLab","description":null,"archived":false,"fork":false,"pushed_at":"2022-03-17T18:10:51.000Z","size":9464,"stargazers_count":1,"open_issues_count":3,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-15T12:45:33.734Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MaayanLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-08-24T15:57:16.000Z","updated_at":"2021-11-17T20:12:41.000Z","dependencies_parsed_at":"2022-09-23T06:21:22.525Z","dependency_job_id":null,"html_url":"https://github.com/MaayanLab/enrichmentAPI","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MaayanLab/enrichmentAPI","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FenrichmentAPI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FenrichmentAPI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FenrichmentAPI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FenrichmentAPI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MaayanLab","download_url":"https://codeload.github.com/MaayanLab/enrichmentAPI/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FenrichmentAPI/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270505938,"owners_count":24596505,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-14T02:00:10.309Z","response_time":75,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-21T09:26:10.448Z","updated_at":"2025-08-15T00:36:25.884Z","avatar_url":"https://github.com/MaayanLab.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# API documentation\n\nThe API contains two main endpoints. One is for generation of new data called ```origin/api/v1/*``` and another endpoint is the primary access point to data queries ```api/v1/*```.\n\nFor a full documentation, please refer to the API documentation:\nhttps://maayanlab.cloud/sigcom/data-api/swagger.html\n\n# Adding data to Signature Commons\n\nSignature Commons can load libraries from a cloud repository on startup if the environmental variable ``` S3_AUTOLOAD ``` is set to ``` 'true' ```. \n\n#### Parameters\n\u003ctable\u003e\n    \u003ctr\u003e\n        \u003ctd\u003e\u003cstrong\u003eName\u003c/strong\u003e\u003c/td\u003e\n        \u003ctd\u003e\u003cstrong\u003eType\u003c/strong\u003e\u003c/td\u003e\n        \u003ctd\u003e\u003cstrong\u003eDescription\u003c/strong\u003e\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003e\u003ccode\u003eapi_key\u003c/code\u003e\u003c/td\u003e\n        \u003ctd\u003estring\u003c/td\u003e\n        \u003ctd\u003eYour own API public key\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003e\u003ccode\u003etimestamp\u003c/code\u003e\u003c/td\u003e\n        \u003ctd\u003einteger\u003c/td\u003e\n        \u003ctd\u003eCurrent unix timestamp (GMT+0) in \u003ca href=\"http://www.epochconverter.com/\"\u003eseconds\u003c/a\u003e\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003e\u003ccode\u003edev_hash\u003c/code\u003e\u003c/td\u003e\n        \u003ctd\u003estring\u003c/td\u003e\n        \u003ctd\u003e\n            Calculate with \u003ccode\u003etimestamp\u003c/code\u003e and \u003ccode\u003eapi_secret\u003c/code\u003e\n            \u003cbr\u003e\n            Formula: \u003ccode\u003emd5(concatenate(\u0026lt;timestamp\u0026gt;, \u0026lt;api_secret\u0026gt;))\u003c/code\u003e\n        \u003c/td\u003e\n    \u003c/tr\u003e\n\u003c/table\u003e\n\n# Deploying to rancher or marathon\n\nWhen launching SigCom it requires several environmental variabls.\n\n\u003ctable\u003e\n    \u003ctr\u003e\n        \u003cth\u003eEnvironmental Variable\u003c/th\u003e\n        \u003cth\u003eDescription\u003c/th\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003eTOKEN\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'pass code needed for several API endpoints'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003ePREFIX\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'/sigcom/data-api'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003eJAVA_OPTS\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'-Xmx30G -XX:PermSize=13G -XX:MaxPermSize=13G -XX:+UseCompressedOops'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003edeployment\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'marathon_deployed'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003eAWS_ACCESS_KEY_ID\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'access key id'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003eAWS_SECRET_ACCESS_KEY\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'aws key with S3 credentials to upload new data to AWS bucket'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003eAWS_ENDPOINT_URL\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'http://s3.amazonaws.com'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003eAWS_BUCKET_PREFIX\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'sigcom/'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003eAWS_BUCKET\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'name of bucket'\u003c/td\u003e\u003c/tr\u003e\n    \u003ctr\u003e\u003ctd\u003e\u003ccode\u003eS3_AUTOLOAD\u003c/code\u003e\u003c/td\u003e\u003ctd\u003e'true/false'\u003c/td\u003e\u003c/tr\u003e\n\u003c/table\u003e   \n    \n\n\n# Installation and docker packaging\n\n## Build with Gradle\n### Important tasks\n\n\u003ctable\u003e\n    \u003ctr\u003e\n        \u003cth\u003eTask Name\u003c/th\u003e\n        \u003cth\u003eDescription\u003c/th\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003ewar\u003c/td\u003e\n        \u003ctd\u003eAssembles the application WAR file and saves it in the \u003ci\u003e/docker\u003c/i\u003e directory\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003etomcatRunWar\u003c/td\u003e\n        \u003ctd\u003eStarts a Tomcat instance and deploys the WAR to it\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003eclean\u003c/td\u003e\n        \u003ctd\u003eDeletes the project build directory and files generated by tasks\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003etest\u003c/td\u003e\n        \u003ctd\u003eRuns the unit tests using JUnit or TestNG\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003echeck\u003c/td\u003e\n        \u003ctd\u003eAggregate task that performs verification tasks, such as running the tests\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n        \u003ctd\u003ecompileJava\u003c/td\u003e\n        \u003ctd\u003eCompiles production Java source files using the JDK compiler\u003c/td\u003e\n    \u003c/tr\u003e\n\u003c/table\u003e\n\n### Running tasks\n\nTo run gradle task, enter\n```text\n./gradlew {task_name}\n```\n\n### Documentation\n\n\u003ca href=\"https://docs.gradle.org/current/userguide/java_plugin.html\"\u003eThe Java Plugin documentation\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://docs.gradle.org/current/userguide/war_plugin.html\"\u003eThe War Plugin documentation\u003c/a\u003e\u003cbr\u003e\n\u003ca href=\"https://github.com/bmuschko/gradle-tomcat-plugin\"\u003eThe Tomcat Plugin documentation\u003c/a\u003e\n\n### Testing locally\nThis will launch the enrichment API on the local machine and should be accessible through the localhost.\n```text\n./gradlew tomcatRunWar\n```\n\n### Stoping gradle process\nProcesses need to be stopped manually if timcatRunWar has previously been executed.\n```text\n./gradlew stop\n```\n\n### Docker-compose\nGetting started with docker-compose\n\n```bash\ngradle war\ndocker-compose build\ndocker-compose up\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fenrichmentapi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaayanlab%2Fenrichmentapi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fenrichmentapi/lists"}